Problem Set 1

Use the links and their instructions from the Applications section to help answer the following questions.

1. Find the nucleotide sequences of the following genes:

a. Human ornithine aminotransferase (OAT), nuclear gene encoding mitochondrial protein

b. YEL076C gene in chromosome V of Saccharomyces cerevisiae.

c. CDC13p, Saccharomyces cerevisiae single-stranded telomeric binding protein.

d. Homo sapiens herpesvirus protein B (HVEB) mRNA

e. Simian immunodeficiency virus of Chimpanzee (Pan troglodytes), related to HIV.

2. Find the possible origin and gene function of the following nucleotide sequences:

a. Sequence 1

CACGGTGATCAAAGTGAGAATGAGCTCCCAGGATTGGGGGGCAAGGAAGATAGGAGGGTCAAACAGAGTCGGGGAGAAGCCAGGGA
GAGCTACAGAGAAACCGGGTCCAGCAGAGCAAGTGATGAGAGAGCTGCCCATCTTCCAACCAGCACACCCCTAGACATTGACACTG
CATCGGAGTCAGGCCAAGATCCGCAGGACAGTCGAAGGTCAGCTGACGCCCTGCTCAGGCTGCAAGCCATGGCAGGAATCTTGGAG
GAACAAGGCTCAGACACGGACACCCCTAGGGTG

b. Sequence 2

CCCTGTGGAGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAGCAGGGAGGGCAGGAGCCAGGGCTGGGCATAAAAGTCAGGGC
AGAGCCATCTATTGCTTACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCACCTGACTCCTG
AGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTTGGTATCAAGG
TTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAGAGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTC
TCTGCCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGGTGATCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTG
TCCACTCCTGATGCTGTTATGGG

c. Sequence 3

AGTACGGTACACCAATTATTTTGAAGGCCGCTTATGGAGGAGGTGGTCGTGGAATTCGTCGTGTTGATAAATTGGAAGAAGTTGA
AGAGGCATTCCGTAGATCCTACTCGGAAGCTCAAGCTGCGTTTGGAGACGGAAGTCTTTTCGTTGAAAAGTTTGTTGAGAGACCA
AGACATATTGAAGTTCAGCTGCTTGGAGACCATCATGGAAATATTGTTCATTTGTATGAGCGTGATTGTTCAGTGCAACGTCGTC
ATCAAAAGGTTGTTGAAATTGCTCCAGCGCCAGCTCTCCCAGAAGGTGTTCGTGAGAAAATTTTGGCAGACGCTCTTCGACTTGC
AAGACATGTTGGATACCAAAATGCTGGTACAGTCGAATTCCTGGTTGATCAGAAGGGCAACTACTATTTCATCGAAGTGAATGCA
CGTCTTCAAGTCGAGCATACAGTAACTGAAGAGATCACTGGTGTGGATCTTGTCCAAGCTCAAATTCGTATCGCCGAAGGAAAAT
CTCTGGATGATCTGAAGCTTTCACAGGAAACTATTCAAACTACTGGCTCAGCTATTCAATGTCGTGTCACAACTGAAGATCCAGC
TAAAGGATTCCAGCCAGATTCCGGAAGAATTGAAGTTTTCCGATCCGGAGAGGGAATGGGAATTCGTCTTGATTCAGCATCTGCC
TTCGCAGGATCAGTCATTTCACCTCACTACGATTCTTTGATGGTCAAAGTAATTGCATCGGCTAGAAATCATCCGAACGCTGCCG
CAAAAATGATTCGTGCCCTCAAAAAGTTCCGTATCCGAGGCGTAAAGACAAACATCCCATTTCTGCTCAACGTTCTTCGCCAGCC
CAGCTTCCTTGATGCATCCGTCGATACGTATTTCATTGATGAGCATCCAGAGTTGTTCCAATTCAAACCAAGCCAAAACCGTGCT
CAAAAGTTGTTGAACTATTTGGGAGAAGTTAAGGTGAACGGTCCAACTACTCCTCTTGCTACTGACCTGAAACCAGCAGTTGTTT

3. Align the following sequences (single sequence alignment):

a. Sequence 1

CAGGGGCAGTGCGGGAGGTGCTGGGCTTTCTCAACAGCTGAGGTGATTTCCGATCGAACATGTATTGCAA
GCAATGGTACCCAACAACCAATCATCTCCCCAACTGATCTGCTCACTTGTTGTGGAATGTCATGCGGAGA
GGGCTGTAACGGCGGCTAT

b. Sequence 2

ATGTCTACTATTCCATCAGAAATAATCAATTGGACAATTTTGAACGAGATAATTTCCATGGATGACGATG
ACAGTGATTTTAGCAAAGGATTAATCATTCAATTCATAGATCAGGCTCAAACCACGTTTGCACAAATGCA
GAGACAACTAGACGGCGAAAAGAATCTTACTGAACTGGATAACTTGGGGCATTTCTTAAAAGGATCGTCT
GCCGCGCTCGGCTTGCAAAGGATCGCTTGGGTTTGTGAGCGTATTCAGAATTTAGGGAGAAAGATGGAAC
ACTTTTTCCCTAACAAAACAGAACTAGTAAATACCCTTTCAGATAAGTCCATTATAAATGGAATCAACAT
TGACGAGGATGATGAAGAAATAAAAATTCAAGTCGACGATAAAGATGAAAATAGTATCTATTTGATTTTA
ATAGCAAAGGCCCTGAACCAATCTCGATTGGAGTTTAAATTAGCTAGAATTGAACTATCAAAGTACTATA
ATACTAATCTT

c. Sequence 3

ATTCTTTTGAGTCGGGAGAACTAGGTAACAATTCGGAAACTCCAAAGGGTGGATGAGGGGCGCGCGGGGT
GTGTGTGGGGGATACTCTGGTCCCCCGTGCAGTGACCTCTAAGTCAGAGGCTGGCACACACACACCTTCC
ATTTTTTCCCAACCGCAGGATGGCGCCTCATCCCTTGGATGCGCTCACCATCCAAGTGTCCCCAGAGACA
CAACAACCTTTTCCCGGAGCCTCGGACCACGAAGTGCTCAGTTCCAATTCCACCCCACCTAGCCCCACTC
TCATACCTAGGGACTGCTCCGAAGCAGAAGTGGGTGACTGCCGAGGGACCTCGAGGAAGCTCCGCGCCCG
ACGCGGAGGGCGCAACAGGCCCAAGAGCGAGTTGGCACTCAGCAAACAGCGAAGAAGCCGGCGCAAGAAG
GCCAATGATCGGGAGCGCAATCGCATGCACAACCTCAACTCGGCGCTGGATGCGCTGCGCGGTGTCCTGC
CCACCTTCCCGGATGACGCCAAACTTACAAAGATCGAGACCCTGCGCTTCGCCCACAACTACATCTGGGC
ACTGACTCAGACGCTGCGCATAGCGGACCACAGCTTCTATGGCCCGGAGCCCCCTGTGCCCTGTGGAGAG
CTGGGGAGCCCCGGAGGTGGCTCCAACGGGGACTGGGGCTCTATCTACTCCCCAGTCTCCCAAGCGGGTA
ACCTGAGCCCCACGGCCTCATTGGAGGAATTCCCTGGCCTGCAGGTGCCCAGCTCCCCATCCTATCTGCT
CCCGGGAGCACTGGTGTTCTCAGACTTCTTGTGAAGAGACCTGTCTGGCTCTGGGTGGTGGGTGCTAGTG
GAAAGGGAGGGGACCACAGCC

4. Translate the following nucleotide sequences in 3 reading frames:

a. Sequence 1

CACGGTGATCAAAGTGAGAATGAGCTCCCAGGATTGGGGGGCAAGGAAGATAGGAGGGTCAAACAGAGTCGGGGAGAAGCCAGGGA
GAGCTACAGAGAAACCGGGTCCAGCAGAGCAAGTGATGAGAGAGCTGCCCATCTTCCAACCAGCACACCCCTAGACATTGACACTG
CATCGGAGTCAGGCCAAGATCCGCAGGACAGTCGAAGGTCAGCTGACGCCCTGCTCAGGCTGCAAGCCATGGCAGGAATCTTGGAG
GAACAAGGCTCAGACACGGACACCCCTAGGGTG

b. Sequence 2

CAGGGGCAGTGCGGGAGGTGCTGGGCTTTCTCAACAGCTGAGGTGATTTCCGATCGAACATGTATTGCAA
GCAATGGTACCCAACAACCAATCATCTCCCCAACTGATCTGCTCACTTGTTGTGGAATGTCATGCGGAGA
GGGCTGTAACGGCGGCTAT

c. Sequence 3

CCCTGTGGAGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAGCAGGGAGGGCAGGAGCCAGGGCTGGGCATAAAAGTCAGGGC
AGAGCCATCTATTGCTTACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCACCTGACTCCTG
AGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTTGGTATCAAGG
TTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAGAGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTC
TCTGCCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGGTGATCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTG
TCCACTCCTGATGCTGTTATGGG

5. Find three article/journal citations for each the following topics:

a. Nanotechnology in medicine and the biological sciences.

b. Human Immunodeficiency Virus (HIV).

6. Does the restriction enzyme XhoI cut this sequence, and if so how many times does it cut, where does it cut (give approx. base pair region), and does the cut leave a blunt ends or a staggered ends?

ATTCTTTTGAGTCGGGAGAACTAGGTAACAATTCGGAAACTCCAAAGGGTGGATGAGGGGCGCGCGGGGT
GTGTGTGGGGGATACTCTGGTCCCCCGTGCAGTGACCTCTAAGTCAGAGGCTGGCACACACACACCTTCC
ATTTTTTCCCAACCGCAGGATGGCGCCTCATCCCTTGGATGCGCTCACCATCCAAGTGTCCCCAGAGACA
CAACAACCTTTTCCCGGAGCCTCGGACCACGAAGTGCTCAGTTCCAATTCCACCCCACCTAGCCCCACTC
TCATACCTAGGGACTGCTCCGAAGCAGAAGTGGGTGACTGCCGAGGGACCTCGAGGAAGCTCCGCGCCCG
ACGCGGAGGGCGCAACAGGCCCAAGAGCGAGTTGGCACTCAGCAAACAGCGAAGAAGCCGGCGCAAGAAG
GCCAATGATCGGGAGCGCAATCGCATGCACAACCTCAACTCGGCGCTGGATGCGCTGCGCGGTGTCCTGC
CCACCTTCCCGGATGACGCCAAACTTACAAAGATCGAGACCCTGCGCTTCGCCCACAACTACATCTGGGC
ACTGACTCAGACGCTGCGCATAGCGGACCACAGCTTCTATGGCCCGGAGCCCCCTGTGCCCTGTGGAGAG
CTGGGGAGCCCCGGAGGTGGCTCCAACGGGGACTGGGGCTCTATCTACTCCCCAGTCTCCCAAGCGGGTA
ACCTGAGCCCCACGGCCTCATTGGAGGAATTCCCTGGCCTGCAGGTGCCCAGCTCCCCATCCTATCTGCT
CCCGGGAGCACTGGTGTTCTCAGACTTCTTGTGAAGAGACCTGTCTGGCTCTGGGTGGTGGGTGCTAGTG
GAAAGGGAGGGGACCACAGCC

7. Determine the restriction digest map of the following sequence with restriction enzymes that recognize six base pair sequences.

>gi|7524758|ref|NC_001776.1|| Oryza sativa mitochondrial plasmid B2, complete sequence

 
CCGAGGTACCAGAGGATAGCCTTTAGGATATCCGTCGGTAGGAGATATCGAGTCGTTAGAGCACATATCT
CCGTGATCCCTTCCACAGCTAAACGTAGATCTCTATCTTGTAGTGGAGTGTAGAGTAAAGATATACCGGA
GTGGAGTGCAAGAAGGTTATAGGGGAGTGTGGCGCCCGTTGCCCGCCTTTCGTCTCGGTTGAAAAACAAA
ACTGTTGCTTGTTTTGTTCATTCAAGTAGTGGTTTAGCCCTCGAATCTATAGCGAAAGAGTTAGCTCAAC
CTATCTACTACTACCCTTGGAAAGGGGGTGTGTGTGGTATACCCGTTACGACTCCCCTCGAACTGAGCCA
TTTTCATGATTTTACAATCAAAGAAAGTTCCATACTTTTTTATTCCCGGTATGGAGCCAACGTCGCTTCG
CTTTCGCAGGACAATTTCCTTCTGGAAAAATATCCAGTGGCATATCCCATCTAGCTCTGGGAATCTTTCC
ACAACCAGCGCCTTCTTGTCCGATGAAGTTCAAGTCTCTAACCTGTTCTTGCCCGGGAATGTCCCTCCTT
CGAACTCGAAGTCAGAGTTTTCCGGTTATCCGATGGGCGATTTATGATAGTTCCGATGCACTTCTCATGC
TAGCCTATCGACAAGATCAGGGTTCAACTACTGTTGCCTCAACGGGTTCGCTGGTCACTTTAACAGTTTT
TTAAGCAGGCATTTTCGTGGTTCTCGTCATATAAACCAGTCAGGTACTAGCGTGATTTCATGCATTAATC
TATTGCTCGAAGGAACCTTTCGTCAGAAAACTTATTCAAAAGGTACCCGGTGTTCTAGCGCATTTCTGTT
AAGAGAAGTACCCCTTGTAGGCCTGAGATGCCCTCTATCGAGCGATATAACGACGGTTGCTATTTTTAGG
TACACGTGTTTTTTGAAGAAAGCACTTTTAAAAAGGAAAGTAGTAAAATGAAAATACTCAATTTAATAAA
TCCTAAATTATCTGTGGCATTGAATTATGAAAGTAAACACTGAAAGTTTACCACTTACAAAAGTAAATGT
ACTACCCGACTAAAAGGAGGAAATCCAATTAGAGGTGTAAACTCTTTTCTTTTCTATCGAGTAGATTCCC
TTTTATTTATAAATAGTAAACTAACGAATAGATAATTAGTATTCCCTCATATAATTAGTACTAGCTGTTC
CTTCATTAATGGTACGTGTATTCACGAGGGCTCTGCTTCGCTCTATTCCACCTCCCGGGTGTATGGAAAA
ATCTTTAAAAGAAATAAATCATGCGGTACTTCTTGTTTTAATCACTCTTCCTTTCCTCCCGGAACTGGGG
AAGAACCCTTCTGAAAAGGAATGGAGGTCTATCTTTACTCGGAGTGCAACGCAGAGATAGAGATCGAAGA
GCCGCTGTGCTTGGGGACGAGGGGACTCACTCAACCTCAAAGTTGAGGGAATCCCGAAGCCTCGGAATCT
AGCGTTAGCGTAAGG

8. Convert the following protein sequences back to their nucleotide sequences using the correct codon usage table. For example, use the Homo sapien codon usage table if the protein sequence corresponds to a human gene product.

>gi|126001|sp|P00709|LCA_HUMAN ALPHA-LACTALBUMIN PRECURSOR (LACTOSE SYNTHASE B PROTEIN)

MRFFVPLFLVGILFPAILAKQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGL
FQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKILDIKGIDYWLAHKALCTEKLEQWLCEKL

>gi|2119314|pir||I61690 myosin - human (fragment)

CVIISGESGAGKTVAAKYIMSYISRVSGGGTKVQHVKDIILQSNPLLEAFGNAKTVRNNNSSRFGKYFEI
QFSPGGEPDGGKISNFLLEK

>gi|746398|gb|AAA97505.1| ampicillin-binding protein (E. coli)

MRFSRFIIGLTSCIAFSVQAANVDEYITQLPAGANLALMVQKVGASAPAIDYHSQQMALPASTQKVITAL
AALIQLGPDFRFTTTLETKGNVENGVLKGDLVARFGADPTLKRQDIRNMVATLKKSGVNQIDGNVLIDTS
IFASHDKAPGWPWNDMTQCFSAPPAAAIVDRNCFSVSLYSAPKPGDMAFIRVASYYPVTMFSQVRTLPRG
SAEAQYCELDVVPGDLNRFTLTGCLPQRSEPLPLAFAVQDGASYAGAILKDELKQAGITWSGTLLRQTQV
NEPGTVVASKQSAPLHDLLKIMLKKSDNMIADTVFRMIGHARFNVPGTWRAGSDAVRQILRQQAGVDIGN
TIIADGSGLSRHNLIAPATMMQVLQYIAQHDNELNFISMLPLAGYDGSLQYRAGLHQAGVDGKVSAKTGS
LQGVYNLAGFITTASGQRMAFVQYLSGYAVEPADQRNRRIPLVRFESRLYKDIYQNN

>gi|476966|pir||A47398 serotonin transporter - human

METTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYSAVPSPGAGDDTRHSIPATTTTL
VAELHQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELALG
QYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCT
NYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKV
VWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASY
NKFNNNCYQDALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPAS
TFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVK
LLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLMSP
PQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETPTEIPCGDIRLNAV

9. Determine all possible properties of the 4 protein sequences from Problem #8. Molecular weight, isoelectric point, extinction coefficients, titration curve, etc.

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